def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
try:
frag1_coords, frag1_mol = rdkit_util.load_molecule(
mol_pdb_file, is_protein=False, sanitize=True, add_hydrogens=False)
frag2_coords, frag2_mol = rdkit_util.load_molecule(
protein_pdb_file, is_protein=True, sanitize=True, add_hydrogens=False)
except MoleculeLoadException:
# Currently handles loading failures by returning None
# TODO: Is there a better handling procedure?
logging.warning("Some molecules cannot be loaded by Rdkit. Skipping")
return None
system_mol = rdkit_util.merge_molecules([frag1_mol, frag2_mol])
system_coords = rdkit_util.get_xyz_from_mol(system_mol)
frag1_coords, frag1_mol = self._strip_hydrogens(frag1_coords, frag1_mol)
frag2_coords, frag2_mol = self._strip_hydrogens(frag2_coords, frag2_mol)
system_coords, system_mol = self._strip_hydrogens(system_coords, system_mol)
try:
frag1_coords, frag1_neighbor_list, frag1_z = self.featurize_mol(
frag1_coords, frag1_mol, self.frag1_num_atoms)
frag2_coords, frag2_neighbor_list, frag2_z = self.featurize_mol(
frag2_coords, frag2_mol, self.frag2_num_atoms)
system_coords, system_neighbor_list, system_z = self.featurize_mol(
system_coords, system_mol, self.complex_num_atoms)
except ValueError as e:
logging.warning(
"max_atoms was set too low. Some complexes too large and skipped")
return None
return frag1_coords, frag1_neighbor_list, frag1_z, frag2_coords, frag2_neighbor_list, frag2_z, \
system_coords, system_neighbor_list, system_z
def test_get_xyz_from_mol(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf")
xyz, mol = rdkit_util.load_molecule(
ligand_file, calc_charges=False, add_hydrogens=False)
xyz2 = rdkit_util.get_xyz_from_mol(mol)
equal_array = np.all(xyz == xyz2)
assert_true(equal_array)
def test_load_docked_ligand(self):
docked_ligands, scores = vina_utils.load_docked_ligands(
self.docked_ligands)
assert len(docked_ligands) == 9
assert len(scores) == 9
for ligand, score in zip(docked_ligands, scores):
xyz = rdkit_util.get_xyz_from_mol(ligand)
assert score < 0 # This is a binding free energy
assert np.count_nonzero(xyz) > 0
def test_get_xyz_from_mol(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
ligand_file = os.path.join(current_dir,
"../../dock/tests/1jld_ligand.sdf")
xyz, mol = rdkit_util.load_molecule(ligand_file,
calc_charges=False,
add_hydrogens=False)
xyz2 = rdkit_util.get_xyz_from_mol(mol)
equal_array = np.all(xyz == xyz2)
assert equal_array
def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
frag1_coords, frag1_mol = rdkit_util.load_molecule(mol_pdb_file)
frag2_coords, frag2_mol = rdkit_util.load_molecule(protein_pdb_file)
system_mol = rdkit_util.merge_molecules(frag1_mol, frag2_mol)
system_coords = rdkit_util.get_xyz_from_mol(system_mol)
frag1_coords, frag1_mol = self._strip_hydrogens(frag1_coords, frag1_mol)
frag2_coords, frag2_mol = self._strip_hydrogens(frag2_coords, frag2_mol)
system_coords, system_mol = self._strip_hydrogens(system_coords, system_mol)
frag1_coords, frag1_neighbor_list, frag1_z = self.featurize_mol(
frag1_coords, frag1_mol, self.frag1_num_atoms)
frag2_coords, frag2_neighbor_list, frag2_z = self.featurize_mol(
frag2_coords, frag2_mol, self.frag2_num_atoms)
system_coords, system_neighbor_list, system_z = self.featurize_mol(
system_coords, system_mol, self.complex_num_atoms)
return frag1_coords, frag1_neighbor_list, frag1_z, frag2_coords, frag2_neighbor_list, frag2_z, \
system_coords, system_neighbor_list, system_z
def _featurize_complex(self, mol_pdb_file, protein_pdb_file):
frag1_coords, frag1_mol = rdkit_util.load_molecule(mol_pdb_file)
frag2_coords, frag2_mol = rdkit_util.load_molecule(protein_pdb_file)
system_mol = rdkit_util.merge_molecules(frag1_mol, frag2_mol)
system_coords = rdkit_util.get_xyz_from_mol(system_mol)
frag1_coords, frag1_mol = self._strip_hydrogens(frag1_coords, frag1_mol)
frag2_coords, frag2_mol = self._strip_hydrogens(frag2_coords, frag2_mol)
system_coords, system_mol = self._strip_hydrogens(system_coords, system_mol)
frag1_coords, frag1_neighbor_list, frag1_z = self.featurize_mol(
frag1_coords, frag1_mol, self.frag1_num_atoms)
frag2_coords, frag2_neighbor_list, frag2_z = self.featurize_mol(
frag2_coords, frag2_mol, self.frag2_num_atoms)
system_coords, system_neighbor_list, system_z = self.featurize_mol(
system_coords, system_mol, self.complex_num_atoms)
return frag1_coords, frag1_neighbor_list, frag1_z, frag2_coords, frag2_neighbor_list, frag2_z, \
system_coords, system_neighbor_list, system_z